ihtm-targets-template/README.Rmd at main · OxfordIHTM/ihtm-targets-template · GitHub

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---
output: github_document
---

<!-- README.md is generated from README.Rmd. Please edit that file -->

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
```

# A template R workflow for general data analysis

<!-- badges: start -->
<!-- badges: end -->

This repository is a template for a [`docker`](https://www.docker.com/get-started)-containerised, [`{targets}`](https://docs.ropensci.org/targets/)-based, [`{renv}`](https://rstudio.github.io/renv/articles/renv.html)-enabled [`R`](https://cran.r-project.org/) workflow for general data analysis.

## About the Project

[A DESCRIPTION OF THE PROJECT GOES HERE]

## Repository Structure

The project repository is structured as follows:

```
ihtm-targets-template
    |-- .github/
    |-- R/
    |-- data-raw/
    |-- data/
    |-- outputs/
    |-- renv
    |-- reports
    |-- .Rprofile
    |-- _targets.R
    |-- packages.R
    |-- renv.lock
```

* `.github` contains project testing and automated deployment of outputs workflows via continuous integration and continuous deployment (CI/CD) using Github Actions.

* `R/` contains functions developed/created specifically for use in this workflow.

* `data-raw/` contains raw datasets, usually either downloaded from source or added manually, that are used in the project.

* `data/` contains intermediate and final data outputs produced by the workflow.

* `outputs/` contains compiled reports and figures produced by the workflow.

* `renv/` contains `renv` package specific files and directories used by the package for maintaining R package dependencies within the project. The directory `renv/library`, is a library that contains all packages currently used by the project. This directory, and all files and sub-directories within it, are all generated and managed by the `renv` package. Users should not change/edit these manually.

* `reports/` contains literate code for R Markdown and/or Quarto reports rendered in the workflow.

* `.Rprofile` file is a project R profile generated when initiating `renv` for the first time. This file is run automatically every time R is run within this project, and `renv` uses it to configure the R session to use the `renv` project library.

* `_targets.R` file defines the steps in the workflow's data ingest, data processing, data analysis, and reporting pipeline.

* `packages.R` file lists out all R package dependencies required by the workflow.

* `renv.lock` file is the `renv` lockfile which records enough metadata about every package used in this project that it can be re-installed on a new machine. This file is generated by the `renv` package and should not be changed/edited manually.

## Reproducibility

### R version

This project is built using `R 4.6.1`. To manage R versions, it is recommended to use [`rig`](https://github.com/r-lib/rig) - an R installation manager - to be able to install multiple versions of R and switch between them as needed.

### R package dependencies

This project uses the `{renv}` framework to record R package dependencies and versions. Packages and versions used are recorded in `renv.lock` and code used to manage dependencies is in the `renv` directory and other files in the root project directory.

On starting an R session in the working directory of this repository, first run

```R
renv::restore()
```

to install R package dependencies. This is only done once when the project is being initiated for the first time by a user.

### The workflow

The current workflow has the following steps:

```{r full-workflow, echo = FALSE, results = "asis"}
cat(
  c(
    "```mermaid",
    targets::tar_mermaid(
      targets_only = TRUE, outdated = FALSE, legend = FALSE, color = FALSE
    ),
    "```"
  ),
  sep = "\n"
)
```

## Authors

[LIST OF AUTHORS GOES HERE]

## License

[LICENSE INFORMATION GOES HERE]

## Citation

[CITATION INFORMATION GOES HERE]